Gene annotation pipeline for bacteria
Entering edit mode
4.2 years ago
bird77 ▴ 70

I have a draft genome of a alpha-proteobacterium (genome size about 8Mbp) and I want to perform gene prediction and annotation.

Until now, I have used the RAST server for this task, but the amount of predicted genes with the annotation "hypothetical protein" is very high (about 60%).

What can you recommend for prokaryotic gene prediction and annotation workflows (I certainly can also combine different tools for gene prediction and annotation, but I do not know what the current standard is)?

Thank you so much for your assistance.

annotation genome • 1.8k views
Entering edit mode
4.2 years ago
colindaven ★ 2.7k

Have a look at Prokka by Torsten Seeman, or the recent Genix.

Other places also have web based annotation pipelines, the NCBI one probably still exists.

Entering edit mode
3.2 years ago
predeus ★ 1.6k

Prokka is probably most used in the field now. Using --proteins with a specific database (e.g. species-specific) seems like a good way to annotate most of the ORFs. Just make sure you get the reference proteins in the right format - they need to look something like this:

>gene_id ~~~gene_name~~~putative protein function

There are few scripts to make your protein annotations look like this. the problem is discussed in one of the issues on Prokka github repository.


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